To understand the impacting law of lightweight aggregate moisture content on the cement paste pore structure and its relationship with humidity and deformation of the lightweight aggregate concrete, it is necessary to study the effect of water absorptivity and pre-wet moisture content of lightweight aggregate on the pore structure interfacial transition zone (ITZ) cement paste. The experimental results indicated that the species and moisture content of lightweight aggregate have a greater effect on the pore structure in interfacial transition zone of cement paste in low w/c concrete than that in high w/c concrete. With the saturation level of lightweight aggregate increased, the overall pore structure shows a refinement tendency. The porosity and the larger pore of ITZ in ordinary aggregate are notably higher than those in the basal body cement paste. Meanwhile, we find that the pore structure of ITZ in lightweight aggregate concrete is much different from that in ordinary aggregate concrete. Especially in the concrete using the lightweight aggregate with a high absorption–desorbtion water rate, the pore aperture in ITZ is significantly lower than that in the cement paste, the pore content below 50nm can reach as high as 80%.